What year is your KX65? The stock 02 pipe is much improved and the port timing is way different. Kaw raised the exhaust a bit and reshaped the downward angle of the lower intake port.
Overall the 2002 is much improved in stock form. For the 2000 & 01 models, the problem is in the cylinder porting. The transfers are too large so the aftermarket pipe manufacturers focused on rapid evacuation of the cylinder. That should help the mid range on the older models.
Regarding your DEP pipe, maybe you ddn't jet it rich enough on the slow jet, that could account for the lack of low end.
If anyone has experience running the Pro Circuit kit, please give this member the info he's looking for.
Good luck, Eric